They were hoping to be the last of some 50,000 people to pass through the union Buildings on Friday, where the former president's body has lain.
Officials say at least 100,000 people have visited the venue over the past three days to pay their respects.
Mr Mandela's coffin was taken from the building shortly after doors closed. The coffin was escorted by a guard of honour to a waiting hearse as military helicopters circled over the city.
The body will remain in Pretoria overnight, and there will be a ceremony at a local air force base on Saturday morning to allow members of the governing African National Congress to say a last farewell.
The coffin will then be flown to the Eastern Cape ahead of the burial at Mr Mandela's ancestral home in Qunu on Sunday.
The funeral will mark the end of a period of commemorations in South Africa since the 95-year-old's death on 5 December.
Long queues "The third day closed with over 50,000 paying their respects to our national icon and first democratically elected President of our country," the South African government said in a statement.
Shortly before the lying in state came to an end, at 17:45 local time (15:45 GMT), hundreds of people towards the front of the queue pushed through in the hope to be one of the last through the door.
One police officer told the reporters: "There are too many people. The whole of the Republic of South Africa wants to say goodbye."
Many people waited in the line for 11 hours for the chance to see Nelson Mandela's body.
Some were angry more time had not been allowed for this ceremonial; others said even if they could not reach his coffin for a personal farewell it was enough simply to be there.
Mr Mandela's body could be seen through a glass screen, dressed in one of his trademark patterned shirts.
At each end of the casket stood two navy officers clad in white uniforms, with their swords pointing down.
Lt-Gen Xolani Mabangu, from the defence force, said chief mourners among the Madiba clan and Mandela family, as well as senior government officials, would accompany the body as it travels from Pretoria to the Eastern Cape, the South African Press Association reports.
A military guard of honour will welcome the arrival in Mthatha, and the coffin will be placed on a gun carriage and transported to a hearse.
Local people will form a 'human chain' between Mthatha and Qunu as the procession passes. once in Qunu, the Thembu community will conduct a traditional ceremony.
According to South Africa's Times newspaper, it is not clear whether the Thembu monarch King Buyelekhaya Dalindyebo will be attending the funeral.
According to custom, he should play a central role in the rituals, it reports.
But the king appears to be unhappy about some aspects of protocol and government ministers and Mandela family members have been meeting him to urgently convince him to be there, it says.
A national day of reconciliation will take place on 16 December when a statue of Mr Mandela will be unveiled at the union Buildings.(ChinaDaily）
新闻资讯：
13日，约有5万民众陆续来到联合大厦瞻仰曼德拉遗容。南非官方称，过去3天瞻仰曼德拉遗容的民众至少有10万人。瞻仰仪式结束后，曼德拉的灵柩在仪仗队护送下转运至灵车上。军用直升机在城市上空盘旋。
接下来，曼德拉遗体还将在南非行政首都茨瓦内度过一晚。14日早晨，当地空军基地将举行仪式，南非现任执政党非洲人国民大会成员作最后告别。之后，遗体将空运至曼德拉的故乡东开普省古努，于15日举行葬礼。
葬礼标志着为期十天的曼德拉国葬的结束。
南非政府在一份声明中说：“第三天有超过5万民众向我们国家的标志和首位民选总统致敬。”
在瞻仰仪式最后一刻当地时间下午17:45，排在队列前的数百人推开警戒，不想错过最后的机会。
一名警察说：“人太多了，南非共和国所有人都想和曼德拉说再见。”
许多人排队11个小时，只为能有机会最后见到曼德拉遗容。
有人为无法如愿而感到愤怒，也有人表示，虽然没有见到曼德拉遗容，但自己去了那里，这就够了。
曼德拉身穿标志性的金黑相间的马迪巴衬衫，平静地躺在覆盖着南非国旗的棺材中。公众可透过玻璃罩瞻仰。
棺材两端各站着两名穿白色制服的海军军官，手持宝剑，剑尖朝下。
据南非通讯社报道，南非一名国防军中将表示，曼德拉的遗体将在家人和官员的陪同下运送至东开普省。
军事仪仗队将在乌姆塔塔迎接曼德拉的遗体，灵柩会放在炮架上运抵灵车。
仪仗队行进时，乌姆塔塔和努之间当地民众将排成“人链”送别曼德拉。到达古努后，腾布王朝部族将举行传统仪式。
南非一家报纸称，尚不清楚腾布王朝国王达林岱波是否会出席葬礼。
依据习俗，他应该在仪式中扮演核心角色。
国王似乎对礼仪的某些方面不满，南非政府官员和曼德拉家族成员已紧急与其见面磋商，说服他到场。
葬礼结束后，南非政府将于12月16日南非和解日在联合大厦前揭幕曼德拉的雕像。
